This idea of calorie intake and expenditure being an epiphenomenon... Taubes certainly does say things that seem to suggest that, but what it would even mean for that to be true?
"Epiphenomenon" is somewhat hyperbolic, but it does make a sensible claim. To make clear what that claim is, it is necessary to think about causal graphs, because intervention in a system to produce a desired result can only be successful if it is based on a correct understanding of how the system works.
"dW/dt = Calories in - calories out", while literally true, carries with it the suggestion that a sufficiently accurate causal graph for this problem is one with two arrows, from input to weight and from output to weight. All you have to do to lose weight is to eat less and/or exercise more.
If the causal model is correct, the predicted result of an intervention will happen. If the predicted result does not happen, the model is wrong.
It seems to be more often the experience than not, that the predicted result does not happen. This brings the model into question.
Causal models make two sorts of claim: the claims that are seen, and the claims that are not seen. The claims that are seen are the variables and the arrows of the model: they claim that these properties of the world exist, and these causal influences exist among them. The claims that are not seen are the absences of variables and arrows. Where there is no arrow, the model claims that there is no direct causal effect. Where there is no variable, the model claims there is no other phenomenon in the world causally relevant to the things being modelled.
To repeat in the face of the failed prediction, "but...input minus output!" is to attend only to the claim that is seen. One of the claims that is not seen in this model is the absence of an arrow from input to output. Suppose we hypothetically add one: suppose that restricting calorie intake makes the body reduce its expenditure also. (Or in concrete terms: skip eating for a day and collapse with exhaustion.) What is now the effect on weight of eating less? That depends on the details and relative magnitudes of how these things influence each other. That is just one example. There are many ways in which "dW/dt = Calories in - calories out" could be embedded in a larger graph for which the claimed remedy for overweight will fail. When they fail, it is not because "dW/dt = Calories in - calories out" is false, but because it is incomplete.
For the case of growing children, where it is was said that they eat because they are growing, rather than growing because they eat, the claimed causal graph appears to be something like this: the body's internal processes of development cause a demand for food; the demand for food causes eating; eating makes materials available for growth; growth is sensed by the body's internal processes of development, which adjusts demand for food accordingly. The causal arrows form a cycle, part of which I've nebulously called "the body's internal processes". There will be an arrow into that node from other internal processes, specifying how fast to grow. (Observe that overfed chidren do not develop normally, but faster; they develop at the same speed and also grow fat.) That is what is driving the cycle, hence the paradoxical sounding "they eat because they are growing, rather than growing because they eat".
Notice that most of these hypothetical causal graphs describe processes internal to the organism and difficult to observe or intervene on, and not all that much is definitively known. This is what makes this a hard problem. It is doubly hard if one does not realise that one must think in these terms to make any progress.
Previously: Mainstream Nutrition Science on Obesity
Edit: In retrospect, I think it maybe should have combined this post with part 3. Unfortunately, the problem of what to do with existing comments makes that hard to fix now.
Taubes first made a name for himself as a low-carb advocate in 2002 with a New York Times article titled "What if It's All Been a Big Fat Lie?" When I first read this article, I was getting extremely suspicious by the second paragraph (emphasis added):
It's one thing to claim that, all else equal, low-carb diets have advantages over low-fat diets. It's another thing to claim you can eat unlimited amounts of fatty foods without gaining weight.
I'd heard of Atkins before but didn't know much about him. I got curious to know more about the man Taubes was casting as the hero who just may have been "right all along," so I popped over to the Wikipedia article on the diet, which says:
The last sentence of this paragraph is helpfully marked "citation needed," leaving an unresolved conflict between whatever Wikipedia editor wrote the paragraph and what the Atkins folks (at least now) claim. I ordered a used copy of the original 1972 edition of Atkins' book through Amazon, and what I found supports the Wikipedia editor. The folks currently in charge of Atkins Nutritionals are white-washing.
The sensational "truly luxurious food without limit" quote in Taubes' article, for example, can be found on page 15 and comes with no context that would make it more reasonable. In fact, lest anyone misunderstand it, it's followed by a statement that "As long as you don't take in carbohydrates, you can eat any amount of this 'fattening' food and it won't put a single ounce of fat on you." (In the book, this is italicized for emphasis.)
Atkins acknowledged that most of the people who used his diet ended up eating less overall, but claimed that some of his patients had lost significant amounts of weight eating 3,000 calories per day or more. In one case, Atkins claimed, a man had lost fifty pounds on a diet of 5,000 calories per day. He attempted to explain this by invoking the fact that extremely low-carbohydrate diets will cause people to excrete ketones (which Atkins referred to as "incompletely burned calories") in their urine. However, as a statement on the Atkins diet put out by the American Medical Association explains:
As far as I can tell, nobody today defends Atkins' original "ketones in the urine" explanation for how his diet supposedly works. It's not entirely clear to me what was going on with the patients Atkins claimed lost weight on a high-calorie diet, but it wouldn't be surprising if a minority of his patients had simply misjudged their caloric intake. In spite of this, Taubes still appears to want to defend Atkins' most extreme claims about people being able to eat unlimited fat without gaining weight.
This isn't entirely obvious when you read his books Good Calories, Bad Calories or Why We Get Fat, which go for a slightly less sensational presentation than the Times article. Nevertheless, in the epilogue to Good Calories, Bad Calories, he claims that "Dietary fat, whether saturated or not, is not a cause of obesity, heart disease, or any other chronic disease of civilization." There's a sense in which that claim might be somewhat plausible, if he meant that it's total calories, not fat per se, that's the main culprit in all those problems. But Taubes also puts a lot of energy (no pun intended) into attacking the mainstream emphasis on calories.
Why We Get Fat, for example, contains claims such as:
No effect? That's a strong claim. And as we'll see in the next two posts, Taubes' evidence for this claim ends up consisting largely on a series of misrepresentations of mainstream nutrition science, which allow him to present his views as the only alternative once he's knocked down his straw men.